Difference between revisions of "Task 9: MSUD - Normal Mode Analysis"

From Bioinformatikpedia
(Atomic Displacement)
(Atomic Displacement)
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[[File:1U5B.pdb.mode7to12plot.png|thumb|Mode 7 Atomic Displacement plot]
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[[File:1U5B.pdb.mode7to12plot.png|thumb|Mode 7 Atomic Displacement plot]]
   
 
= ElNemo =
 
= ElNemo =

Revision as of 20:35, 4 July 2012

WEBnm@

WEBnm@ provides users with a number of different for Normal Mode Analysis of their protein of interest.

Deformation Energies

The deformation energies are energies associated with each node and are inversly related to the amplitude of the protein motion and thereby gives a general idea which motion is the strongest. The eigenvalues plot serves the same purpose.


Mode Index Deformation Energy Mode Index Deformation Energy
7 288.99 14 2957.24
8 407.20 15 2715.91
9 589.17 16 3291.75
10 752.78 17 3543.09
11 842.47 18 3927.68
12 994.58 19 4115.63
13 1727.81 20 4950.67

Eigenvalue plot

Atomic Displacement

The atomic displacement plots show what regions in the protein move the most for the specific mode. Here regions where peaks are clustered are are of paticular interest, as single peaks only represent local flexibility.


Mode 7 Atomic Displacement plot

ElNemo

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